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- PDB-6ner: Synthetic Haliangium ochraceum BMC shell -

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Basic information

Entry
Database: PDB / ID: 6ner
TitleSynthetic Haliangium ochraceum BMC shell
ComponentsBMC-H tandem fusion protein
KeywordsSTRUCTURAL PROTEIN / bacterial microcompartment
Function / homology
Function and homology information


bacterial microcompartment
Similarity search - Function
CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC
Similarity search - Domain/homology
Bacterial microcompartment protein homohexamer
Similarity search - Component
Biological speciesHaliangium ochraceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
AuthorsSutter, M. / McGuire, S. / Aussignargues, C. / Kerfeld, C.A.
CitationJournal: ACS Synth Biol / Year: 2019
Title: Structural Characterization of a Synthetic Tandem-Domain Bacterial Microcompartment Shell Protein Capable of Forming Icosahedral Shell Assemblies.
Authors: Sutter, M. / McGuire, S. / Ferlez, B. / Kerfeld, C.A.
History
DepositionDec 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BMC-H tandem fusion protein
B: BMC-H tandem fusion protein
C: BMC-H tandem fusion protein
D: BMC-H tandem fusion protein
E: BMC-H tandem fusion protein
F: BMC-H tandem fusion protein
G: BMC-H tandem fusion protein
H: BMC-H tandem fusion protein
I: BMC-H tandem fusion protein
J: BMC-H tandem fusion protein
K: BMC-H tandem fusion protein
L: BMC-H tandem fusion protein
M: BMC-H tandem fusion protein
N: BMC-H tandem fusion protein
O: BMC-H tandem fusion protein
P: BMC-H tandem fusion protein
Q: BMC-H tandem fusion protein
R: BMC-H tandem fusion protein
S: BMC-H tandem fusion protein
T: BMC-H tandem fusion protein
U: BMC-H tandem fusion protein
V: BMC-H tandem fusion protein
W: BMC-H tandem fusion protein
X: BMC-H tandem fusion protein
Y: BMC-H tandem fusion protein
Z: BMC-H tandem fusion protein
a: BMC-H tandem fusion protein
b: BMC-H tandem fusion protein
c: BMC-H tandem fusion protein
d: BMC-H tandem fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)655,95140
Polymers654,99030
Non-polymers96110
Water00
1
A: BMC-H tandem fusion protein
B: BMC-H tandem fusion protein
C: BMC-H tandem fusion protein
D: BMC-H tandem fusion protein
E: BMC-H tandem fusion protein
F: BMC-H tandem fusion protein
G: BMC-H tandem fusion protein
H: BMC-H tandem fusion protein
I: BMC-H tandem fusion protein
J: BMC-H tandem fusion protein
K: BMC-H tandem fusion protein
L: BMC-H tandem fusion protein
M: BMC-H tandem fusion protein
N: BMC-H tandem fusion protein
O: BMC-H tandem fusion protein
P: BMC-H tandem fusion protein
Q: BMC-H tandem fusion protein
R: BMC-H tandem fusion protein
S: BMC-H tandem fusion protein
T: BMC-H tandem fusion protein
U: BMC-H tandem fusion protein
V: BMC-H tandem fusion protein
W: BMC-H tandem fusion protein
X: BMC-H tandem fusion protein
Y: BMC-H tandem fusion protein
Z: BMC-H tandem fusion protein
a: BMC-H tandem fusion protein
b: BMC-H tandem fusion protein
c: BMC-H tandem fusion protein
d: BMC-H tandem fusion protein
hetero molecules

A: BMC-H tandem fusion protein
B: BMC-H tandem fusion protein
C: BMC-H tandem fusion protein
D: BMC-H tandem fusion protein
E: BMC-H tandem fusion protein
F: BMC-H tandem fusion protein
G: BMC-H tandem fusion protein
H: BMC-H tandem fusion protein
I: BMC-H tandem fusion protein
J: BMC-H tandem fusion protein
K: BMC-H tandem fusion protein
L: BMC-H tandem fusion protein
M: BMC-H tandem fusion protein
N: BMC-H tandem fusion protein
O: BMC-H tandem fusion protein
P: BMC-H tandem fusion protein
Q: BMC-H tandem fusion protein
R: BMC-H tandem fusion protein
S: BMC-H tandem fusion protein
T: BMC-H tandem fusion protein
U: BMC-H tandem fusion protein
V: BMC-H tandem fusion protein
W: BMC-H tandem fusion protein
X: BMC-H tandem fusion protein
Y: BMC-H tandem fusion protein
Z: BMC-H tandem fusion protein
a: BMC-H tandem fusion protein
b: BMC-H tandem fusion protein
c: BMC-H tandem fusion protein
d: BMC-H tandem fusion protein
hetero molecules

A: BMC-H tandem fusion protein
B: BMC-H tandem fusion protein
C: BMC-H tandem fusion protein
D: BMC-H tandem fusion protein
E: BMC-H tandem fusion protein
F: BMC-H tandem fusion protein
G: BMC-H tandem fusion protein
H: BMC-H tandem fusion protein
I: BMC-H tandem fusion protein
J: BMC-H tandem fusion protein
K: BMC-H tandem fusion protein
L: BMC-H tandem fusion protein
M: BMC-H tandem fusion protein
N: BMC-H tandem fusion protein
O: BMC-H tandem fusion protein
P: BMC-H tandem fusion protein
Q: BMC-H tandem fusion protein
R: BMC-H tandem fusion protein
S: BMC-H tandem fusion protein
T: BMC-H tandem fusion protein
U: BMC-H tandem fusion protein
V: BMC-H tandem fusion protein
W: BMC-H tandem fusion protein
X: BMC-H tandem fusion protein
Y: BMC-H tandem fusion protein
Z: BMC-H tandem fusion protein
a: BMC-H tandem fusion protein
b: BMC-H tandem fusion protein
c: BMC-H tandem fusion protein
d: BMC-H tandem fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,967,853120
Polymers1,964,97190
Non-polymers2,88230
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Unit cell
Length a, b, c (Å)325.513, 325.513, 325.513
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein ...
BMC-H tandem fusion protein


Mass: 21833.012 Da / Num. of mol.: 30
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliangium ochraceum (bacteria) / Gene: Hoch_5815 / Production host: Escherichia coli (E. coli) / References: UniProt: D0LID5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.39 Å3/Da / Density % sol: 71.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 8.0, 2% tryptone [w/v], 14% [w/v] PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.59→49.64 Å / Num. obs: 133312 / % possible obs: 100 % / Redundancy: 40.4 % / CC1/2: 0.938 / Rmerge(I) obs: 0.581 / Net I/σ(I): 8.7
Reflection shellResolution: 3.59→3.65 Å / Redundancy: 38.8 % / Rmerge(I) obs: 4.073 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6556 / CC1/2: 0.808 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DJB

5djb


Resolution: 3.59→49.64 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2102 1676 1.26 %
Rwork0.1708 --
obs0.1713 133107 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.59→49.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39460 0 50 0 39510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00139974
X-RAY DIFFRACTIONf_angle_d0.34454251
X-RAY DIFFRACTIONf_dihedral_angle_d7.11824019
X-RAY DIFFRACTIONf_chiral_restr0.0416528
X-RAY DIFFRACTIONf_plane_restr0.0027135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5901-3.69570.30471380.278310867X-RAY DIFFRACTION100
3.6957-3.81490.31041420.244710911X-RAY DIFFRACTION100
3.8149-3.95120.30881400.245210797X-RAY DIFFRACTION100
3.9512-4.10940.29371400.224310952X-RAY DIFFRACTION100
4.1094-4.29630.23821390.197810881X-RAY DIFFRACTION100
4.2963-4.52270.23691330.17810925X-RAY DIFFRACTION100
4.5227-4.80580.20571390.160610894X-RAY DIFFRACTION100
4.8058-5.17650.19131400.138310934X-RAY DIFFRACTION100
5.1765-5.69680.17981440.148310998X-RAY DIFFRACTION100
5.6968-6.51950.18761410.161510971X-RAY DIFFRACTION100
6.5195-8.20790.16131420.138411057X-RAY DIFFRACTION100
8.2079-49.6450.17641380.146211244X-RAY DIFFRACTION100

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